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Compared to japonica, the lower genetic transformation efficiency of indica is a technical bottleneck for rice molecular breeding. Specifically, callus browning frequently occurs during the culture of the elite indica variety 93-11, leading to poor culturability and lower genetic transformation efficiency. Here, 67 QTLs related to culturability were detected using 97 introgression lines (designated as 9DILs) derived from Dongxiang common wild rice (DXCWR, Oryza rufipogon Griff.) with 93-11 genetic background, explaining 4% ~12% of the phenotypic variations. The QTL qCBT9 on chromosome 9 was a primary QTL for reducing callus browning derived from DXCWR. Five 9DILs with light callus browning and high differentiation were screened. We evaluated the callus browning index (CBI) of 100 F2 population crossed of 93-11 and 9DIL71 and the recombinant plants screened from 3270 individuals. The qCBT9 was delimited to a ~148kb region between the markers X16 and X23. RNA-seq analysis of DEGs between 9DIL71 and 93-11 showed three upregulated DEGs (Os09g0526500, Os09g0527900, Os09g0528200,) and three downregulated DEGs (Os09g0526700, Os09g0526800, Os09g0527700) were located in the candidate region of qCBT9. Furthermore, callus browning may be involved in cell senescence and death caused by oxidative stress. The differentiation of indica and japonica in this region suggested that qCBT9 was possibly a vital QTL contributed to better culturability of japonica. Our results laid a foundation for further cloning of the gene for reduced callus browning in O. rufipogon, and also provided a new genetic resource and material basis for improving the culturability and genetic transformation efficiency of cultivated rice. [ABSTRACT FROM AUTHOR]

Huamoxiang 3 (HMX3) is a new variety of whole grain black rice that has been bred for its superior taste and nutritional benefits. Whole grain black rice is rich in anthocyanins, which have antioxidant and anti-inflammatory properties. Despite the health benefits of whole grain rice, its consumption remains low worldwide. HMX3 was developed through a breeding program and has been certified as a new variety. It has shown good performance in terms of yield and quality and has received positive feedback from consumers. The nutritional composition of HMX3 is superior to milled grain rice, with higher levels of protein, dietary fiber, amino acids, oil, vitamins, minerals, and bioactive compounds. HMX3 is recommended for late rice cropping in Hubei Province. The research was supported by various grants. [Extracted from the article]

Meeting the ever-increasing food demands of a growing global population while ensuring resource and environmental sustainability presents significant challenges for agriculture worldwide. Arbuscular mycorrhizal symbiosis (AMS) has emerged as a potential solution by increasing the surface area of a plant's root system and enhancing the absorption of phosphorus, nitrogen nutrients, and water. Consequently, there is a longstanding hypothesis that rice varieties exhibiting more efficient AMS could yield higher outputs at reduced input costs, paving the way for the development of Green Super Rice (GSR). Our prior research study identified a variant, OsCERK1DY, derived from Dongxiang wild-type rice, which notably enhanced AMS efficiency in the rice cultivar "ZZ35." This variant represents a promising gene for enhancing yield and nutrient use efficiency in rice breeding. In this study, we conducted a comparative analysis of biomass, crop growth characteristics, yield attributes, and nutrient absorption at varying soil nitrogen levels in the rice cultivar "ZZ35" and its chromosome single-segment substitution line, "GJDN1." In the field, GJDN1 exhibited a higher AM colonization level in its roots compared with ZZ35. Notably, GJDN1 displayed significantly higher effective panicle numbers and seed-setting rates than ZZ35. Moreover, the yield of GJDN1 with 75% nitrogen was 14.27% greater than the maximum yield achieved using ZZ35. At equivalent nitrogen levels, GJDN1 consistently outperformed ZZ35 in chlorophyll (Chl) content, dry matter accumulation, major nutrient element accumulation, N agronomic efficiency (NAE), N recovery efficiency (NRE), and N partial factor productivity (NPFP). The performance of OsCERK1DY overexpression lines corroborated these findings. These results support a model wherein the heightened level of AMS mediated by OsCERK1DY contributes to increased nitrogen, phosphorus, and potassium accumulation. This enhancement in nutrient utilization promotes higher fertilizer efficiency, dry matter accumulation, and ultimately, rice yield. Consequently, the OsCERK1DY gene emerges as a robust candidate for improving yield, reducing fertilizer usage, and facilitating a transition towards greener, lower-carbon agriculture. [ABSTRACT FROM AUTHOR]

Heading date is one of the important agronomic traits that affects rice yield. In this study, we cloned a new rice B3 family gene, OsL1, which regulates rice heading date. Importantly, osl1-1 and osl1-2, two different types of mutants of OsL1 were created using the gene editing technology CRISPR/Cas9 system and exhibited 4 days earlier heading date than that of the wild type under short-day conditions. Subsequently, the plants overexpressing OsL1, OE-OsL1, showed a 2-day later heading date than the wild type in Changsha and a 5-day later heading date in Lingshui, but there was no significant difference in other yield traits. Moreover, the results of subcellular localization study indicated that OsL1 protein was located in the nucleus and the expression pattern analysis showed that OsL1 gene was expressed in rice roots, stems, leaves, and panicles, and the expression level was higher at the root and weak green panicle. In addition, the OsL1 gene was mainly expressed at night time under short-light conditions. The transcriptomic analysis indicated that OsL1 might be involved in the Hd1-Hd3a pathway function. Together, our results revealed that the cloning and functional analysis of OsL1 can provide new strategy for molecular design breeding of rice with suitable fertility period. [ABSTRACT FROM AUTHOR]

Rice grain size is a key determinant of both grain yield and quality. Identification of favorable alleles for use in rice breeding may help to meet the demand for increased yield. In this study, we developed a set of 210 introgression lines (ILs) by using indica variety Huanghuazhan as the donor parent and erect-panicle japonica rice variety Wuyujing3R as the recurrent parent. A total of 133 ILs were selected for high-throughput sequencing. Using specific-locus amplified fragment (SLAF) sequencing technology, 10,103 high-quality SLAF labels evenly distributed on 12 chromosomes were obtained and selected for subsequent analysis. Using a high-density map, quantitative trait locus (QTL) mapping of grain size-related traits was performed, and a total of 38 QTLs were obtained in two environments. Furthermore, qGW2, a novel QTL that controls grain width on chromosome 2, was validated and delimited to a region of 309 kb via substitution mapping. These findings provide new genetic material and a basis for future fine mapping and cloning of favorable QTLs. [ABSTRACT FROM AUTHOR]

Improving quality is an essential goal of rice breeding and production. However, rice quality is not solely determined by genotype, but is also influenced by the environment. Phenotype plasticity refers to the ability of a given genotype to produce different phenotypes under different environmental conditions, which can be a representation of the stability of traits. Seven quality traits of 141 hybrid combinations, deriving from the test-crossing of 7 thermosensitive genic male sterile (TGMS) and 25 restorer lines, were evaluated at 5 trial sites with intermittent sowing of three to five in Southern China. In the Yangtze River Basin, it was observed that delaying the sowing time of hybrid rice combinations leads to an improvement in their overall quality. Twelve parents were identified to have lower plasticity general combing ability (GCA) values with increased ability to produce hybrids with a more stable quality. The parents with superior quality tend to exhibit lower GCA values for plasticity. The genome-wide association study (GWAS) identified 13 and 15 quantitative trait loci (QTLs) associated with phenotype plasticity and BLUP measurement, respectively. Notably, seven QTLs simultaneously affected both phenotype plasticity and BLUP measurement. Two cloned rice quality genes, ALK and GL7, may be involved in controlling the plasticity of quality traits in hybrid rice. The direction of the genetic effect of the QTL6 (ALK) on alkali spreading value (ASV) plasticity varies in different cropping environments. This study provides novel insights into the dynamic genetic basis of quality traits in response to different cropping regions, cultivation practices, and changing climates. These findings establish a foundation for precise breeding and production of stable and high-quality rice. [ABSTRACT FROM AUTHOR]

The grain protein content is an important quality trait in cereals, and the expression level of the OsAAP6 can significantly affect the grain protein content in rice. Through site-directed mutagenesis, we found that the position from −7 to −12 bp upstream of the transcription start site of the OsAAP6 was the functional variation site. By using the yeast single hybrid test, point-to-point in yeast, and the local surface plasmon resonance test, the OsNAC74 was screened and verified to be a regulator upstream of OsAAP6. The OsNAC74 is a constitutively expressed gene whose product is located on the cell membrane. The OsAAP6 and the genes related to the seed storage in the Osnac74 mutants were downregulated, and grain protein content was significantly reduced. In addition, OsNAC74 had a significant impact on quality traits such as grain chalkiness and gel consistency in rice. Although the Osnac74 mutant seeds were relatively small, the individual plant yield was not decreased. Therefore, OsNAC74 is an important regulatory factor with multiple biological functions. This study provides important information for the later use of OsNAC74 gene for molecular design and breeding in rice. [ABSTRACT FROM AUTHOR]

Accurately identifying varieties with targeted agronomic traits was thought to contribute to genetic selection and accelerate rice breeding progress. Genomic selection (GS) is a promising technique that uses markers covering the whole genome to predict the genomic-estimated breeding values (GEBV), with the ability to select before phenotypes are measured. To choose the appropriate GS models for breeding work, we analyzed the predictability of nine agronomic traits measured from a population of 459 diverse rice varieties. By the comparison of eight representative GS models, we found that the prediction accuracies ranged from 0.407 to 0.896, with reproducing kernel Hilbert space (RKHS) having the highest predictive ability in most traits. Further results demonstrated the predictivity of GS is altered by several factors. Moreover, we assessed the method of integrating genome-wide association study (GWAS) into various GS models. The predictabilities of GS combined peak-associated markers generated from six different GWAS models were significantly different; a recommendation of Mixed Linear Model (MLM)-RKHS was given for the GWAS-GS-integrated prediction. Finally, based on the above result, we experimented with applying the P-values obtained from optimal GWAS models into ridge regression best linear unbiased prediction (rrBLUP), which benefited the low predictive traits in rice. [ABSTRACT FROM AUTHOR]

The rapid development of global industrialization has led to serious environmental problems, among which global warming has become one of the major concerns. The gradual rise in global temperature resulted in the loss of food production, and hence a serious threat to world food security. Rice is the main crop for approximately half of the world's population, and its geographic distribution, yield, and quality are frequently reduced due to elevated temperature stress, and breeding rice varieties with tolerance to heat stress is of immense significance. Therefore, it is critical to study the molecular mechanism of rice in response to heat stress. In the last decades, large amounts of studies have been conducted focusing on rice heat stress response. Valuable information has been obtained, which not only sheds light on the regulatory network underlying this physiological process but also provides some candidate genes for improved heat tolerance breeding in rice. In this review, we summarized the studies in this field. Hopefully, it will provide some new insights into the mechanisms of rice under high temperature stress and clues for future engineering breeding of improved heat tolerance rice. [ABSTRACT FROM AUTHOR]

Complete panicle exsertion (CPE) in rice is an important determinant of yield and a desirable trait in breeding. However, the genetic basis of CPE in rice still remains to be completely characterized. An ethyl methane sulfonate (EMS) mutant line of an elite cultivar Samba Mahsuri (BPT 5204), displaying stable and consistent CPE, was identified and named as CPE-110. MutMap and RNA-seq were deployed for unraveling the genomic regions, genes, and markers associated with CPE. Two major genomic intervals, on chromosome 8 (25668481-25750456) and on chromosome 11 (20147154-20190400), were identified to be linked to CPE through MutMap. A non-synonymous SNP (G/A; Chr8:25683828) in the gene LOC_Os08g40570 encoding pyridoxamine 5′-phosphate oxidase with the SNP index 1 was converted to Kompetitive allele-specific PCR (KASP) marker. This SNP (KASP 8-1) exhibited significant association with CPE and further validated through assay in the F2 mapping population, released varieties and CPE exhibiting BPT 5204 mutant lines. RNA-seq of the flag leaves at the booting stage, 1100 genes were upregulated and 1305 downregulated differentially in CPE-110 and BPT 5204. Metabolic pathway analysis indicated an enrichment of genes involved in photosynthesis, glyoxylate, dicarboxylate, porphyrin, pyruvate, chlorophyll, carotenoid, and carbon metabolism. Further molecular and functional studies of the candidate genes could reveal the mechanistic aspects of CPE. [ABSTRACT FROM AUTHOR]

Heading date is a critical agronomic trait that determines crop yield. Although numerous genes associated with heading date have been identified in rice, the mechanisms involving Small Auxin Up RNA (SAUR) family have not been elucidated. In this study, the biological function of several SAUR genes was initially investigated using the CRISPR-Cas9 technology in the Japonica cultivar Zhonghua11 (ZH11) background. Further analysis revealed that the loss-of-function of OsSAUR56 affected heading date in both NLD (natural long-day) and ASD (artificial short-day). OsSAUR56 exhibited predominant expression in the anther, with its protein localized in both the cytoplasm and nucleus. OsSAUR56 regulated flowering time and heading date by modulating the expression of the clock gene OsGI, as well as two repressors Ghd7 and DTH8. Furthermore, haplotype-phenotype association analysis revealed a strong correlation between OsSAUR56 and heading date, suggesting its role in selection during the domestication of rice. In summary, these findings highlights the importance of OsSAUR56 in the regulation of heading date for further potential facilitating genetic engineering for flowering time during rice breeding. [ABSTRACT FROM AUTHOR]

The gelatinization temperature of rice is an important factor in determining the eating and cooking quality, and it affects consumer preference. The alkali digestion value (ADV) is one of the main methods used to test the quality of rice and has a high correlation with the gelatinization temperature. For the development of high-quality rice, it is important to understand the genetic basis of palatability-related traits, and QTL analysis is a statistical method linking phenotypic data and genotype data and is an effective method to explain the genetic basis of variation in complex traits. QTL mapping related to the ADV of brown and milled rice was performed using the 120 Cheongcheong/Nagdong double haploid (CNDH) line. As a result, 12 QTLs related to ADV were detected, and 20 candidate genes were selected from the RM588–RM1163 region of chromosome 6 through screening by gene function analysis. The comparison of the relative expression level of candidate genes showed that OsSS1q6 is highly expressed in CNDH lines with high ADV in both brown rice and milled rice. In addition, OsSS1q6 has high homology with the starch synthase 1 protein and interacts with various starch biosynthesis-related proteins, such as GBSSII, SBE, and APL. Therefore, we suggest that OsSS1q6 identified through QTL mapping could be one of the various genes involved in the gelatinization temperature of rice by regulating starch biosynthesis. This study can be used as basic data for breeding high-quality rice and provides a new genetic resource that can increase the palatability of rice. [ABSTRACT FROM AUTHOR]

As rice is a staple food for nearly half of the world's population, rice varieties with excellent agronomic traits as well as high flavor and nutritional quality such as fragrant rice and purple rice are naturally favored by the market. In the current study, we adopt a fast breeding strategy to improve the aroma and anthocyanin content in the excellent rice inbred line, F25. The strategy skillfully used the advantages of obtaining editing pure lines in T0 generation of CRISPR/Cas9 editing system and easy observation of purple character and grain shape, integrated the subsequent screening of non-transgenic lines, and the elimination of undesirable edited variants from gene-editing and cross-breeding at the same time as the separation of the progeny from the purple cross, thus expediting the breeding process. Compared with conventional breeding strategies, this strategy saves about 6–8 generations and reduces breeding costs. Firstly, we edited the OsBADH2 gene associated with rice flavor using an Agrobacterium-mediated CRISPR/Cas9 system to improve the aroma of F25. In the T0 generation, a homozygous OsBADH2-edited F25 line (F25B) containing more of the scented substance 2-AP was obtained. Then, we crossed F25B (♀) with a purple rice inbred line, P351 (♂), with high anthocyanin enrichment to improve the anthocyanin content of F25. After nearly 2.5 years of screening and identification over five generations, the undesirable variation characteristics caused by gene-editing and hybridization and the transgenic components were screened out. Finally, the improved F25 line with highly stable aroma component, 2-AP, increased anthocyanin content and no exogenous transgenic components were obtained. This study not only provides high-quality aromatic anthocyanin rice lines that meet the market demand, but also offers a reference for the comprehensive use of CRISPR/Cas9 editing technology, hybridization, and marker-assisted selection to accelerate multi-trait improvement and breeding process. [ABSTRACT FROM AUTHOR]

Panicle length (PL) is an important trait that determines panicle architecture and strongly affects grain yield and quality in rice. However, this trait has not been well characterized genetically, and its contribution to yield improvement is not well understood. Characterization of novel genes related to PL is of great significance for breeding high-yielding rice varieties. In our previous research, we identified qPL5, a quantitative trait locus for PL. In this study, we aimed to determine the exact position of qPL5 in the rice genome and identify the candidate gene. Through substitution mapping, we mapped qPL5 to a region of 21.86 kb flanked by the molecular marker loci STS5-99 and STS5-106 in which two candidate genes were predicted. By sequence analysis and relative expression analysis, LOC-Os05g41230, which putatively encodes a BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor, was considered to be the most likely candidate gene for qPL5. In addition, we successfully developed a pair of near-isogenic lines (NILs) for qPL5 in different genetic backgrounds to evaluate the genetic effects of qPL5. Agronomic trait analysis of the NILs indicated that qPL5 positively contributes to plant height, grain number per panicle, panicle length, grain yield per plant, and flag leaf length, but it had no influence on heading date and grain-size-related traits. Therefore, qPL5 and the markers tightly linked to it should be available for molecular breeding of high-yielding varieties. [ABSTRACT FROM AUTHOR]

The japonica rice (Oryza sativa L.) cultivar Koshihikari is considered an important breeding material with good eating quality (EQ). To effectively utilize Koshihikari in molecular breeding programs, determining its whole genome sequence including cultivar-specific segment is crucial. Here, the Koshihikari genome was sequenced using Nanopore and Illumina platforms, and de novo assembly was performed. A highly contiguous Koshihikari genome sequence was compared with Nipponbare, the reference genome of japonica. Genome-wide synteny was observed, as expected, without large structural variations. However, several gaps in alignment were detected on chromosomes 3, 4, 9, and 11. It was notable that previously identified EQ-related QTLs were found in these gaps. Moreover, sequence variations were identified in chromosome 11 at a region flanking the P5 marker, one of the significant markers of good EQ. The Koshihikari-specific P5 region was found to be transmitted through the lineage. High EQ cultivars derived from Koshihikari possessed P5 sequences; on the other hand, Koshihikari-derived low EQ cultivars didn't contain the P5 region, which implies that the P5 genomic region affects the EQ of Koshihikari progenies. The EQ of near-isogenic lines (NILs) of Samnam (a low EQ cultivar) genetic background harboring the P5 segment was improved compared to that of Samnam in Toyo taste value. The structure of the Koshihikari-specific P5 genomic region associated with good EQ was analyzed, which is expected to facilitate the molecular breeding of rice cultivars with superior EQ. [ABSTRACT FROM AUTHOR]

The japonica water-saving and drought-resistance rice (Oryza sativa L.) (WDR) cultivar Huhan 9 harbors genes for resistance to rice blast (Magnaporthe oryzae), including Pi-ta and Pi-b. The early maturing japonica rice cultivar Suhuxiangjing and the high-yield WDR cultivars Huhan 3 and Huhan 11 were used as the parents to conduct single cross breeding and composite hybridization breeding. Strict drought resistance screening was conducted in the segregating generations, the genotypes of which were determined using functional markers of Pi-ta and Pi-b genes. By combining the rapid generation advance of the industrialized breeding system and multi-site shuttle identification, the new WDR cultivar Huhan 106 with early maturity, blast resistance, high yield, and high quality was bred, and it was certified by the Agricultural Crop Variety Certification Commission of Shanghai in 2020. Molecular marker-assisted selection coupled with rapid generation advance and multi-site shuttle identification is a rapid and efficient breeding method for the value-added improvement of crop varieties. [ABSTRACT FROM AUTHOR]

Clubroot disease poses a severe threat to rapeseed (Brassica napus) production worldwide and has recently been spreading across China at an unprecedented pace. Breeding and cultivation of resistant varieties constitute a promising and environment-friendly approach to mitigating this threat. In this study, the clubroot resistance locus PbBa8.1 was successfully transferred into SC4, a shared paternal line of three elite varieties in five generations by marker-assisted backcross breeding. Kompetitive allele specific PCR (KASP) markers of clubroot resistance gene PbBa8.1 and its linked high erucic acid gene (FAE1) were designed and applied for foreground selection, and 1,000 single-nucleotide polymorphisms (SNPs) were selected and used for the background selection. This breeding strategy produced recombinants with the highest recovery ratio of the recurrent parent genome (> 95%) at BC2F2 while breaking the linkage with FAE1 during the selection. An updated version of the paternal line (SC4R) was generated at BC2F3, showing significantly improved clubroot resistance at the seedling stage via artificial inoculation, and was comparable to that of the donor parent. Field trials of the three elite varieties and their updated versions in five environments indicated similar agronomic appearance and final yield. The introduced breeding strategy precisely pyramids the PbBa8.1 and FAE1 loci with the assistance of technical markers in a shorter period and could be applied to other desirable traits for directional improvement in the future. [ABSTRACT FROM AUTHOR]

Genomic selection is an efficient tool for breeding selection, especially for quantitative traits controlled by multiples genes with low heritability. To validate the application of genomic selection in hybrid rice breeding, the yield and grain quality traits of 404 hybrid rice breeding lines were investigated, and the same accessions were genotyped by using a 56 K SNP chip. There were wide variances among the tested accessions for all the measured traits, and most of the traits were correlated. A total of 67 significant loci were identified for the yield-related traits, and 123 significant loci were identified for the grain quality traits by GWAS. Two of these loci associated with increasing grain yield but decreasing grain quality. The GEBVs of all the yield and grain quality traits were calculated by using 15 different prediction algorithms. The plant height, panicle length, thousand grain weight, grain length and width ratio, amylose content, and alkali value have higher predictability than other traits. However, the predictive accuracy of different GS models is different for different traits. This study provided useful information for genomic selection of specific trait using proper markers and prediction models. [ABSTRACT FROM AUTHOR]

Chromosome segment substitution line (CSSL) is important for functional analysis and design breeding of target genes. Here, a novel rice CSSL-Z431 was identified from indica restorer line Xihui18 as recipient and japonica Huhan3 as donor. Z431 contained six segments from Huhan3, with average substitution length of 2.12 Mb. Compared with Xihui18, Z431 increased panicle number per plant (PN) and displayed short-wide grains. The short-wide grain of Z431 was caused by decreased length and increased width of glume cell. Then, thirteen QTLs were identified in secondary F2 population from Xihui18/Z431. Again, eleven QTLs (qPL3, qPN3, qGPP12, qSPP12, qGL3, qGW5, qRLW2, qRLW3, qRLW5, qGWT3, qGWT5-2) were validated by six single-segment substitution lines (SSSLs, S1-S6) developed in F3. In addition, fifteen QTLs (qPN5, qGL1, qGL2, qGL5, qGW1, qGW5-1, qRLW1, qRLW5-2, qGWT1, qGWT2, qYD1, qYD2, qYD3, qYD5, qYD12) were detected by these SSSLs, while not be identified in the F2 population. Multiple panicles of Z431 were controlled by qPN3 and qPN5. OsIAGLU should be the candidate gene for qPN3. The short-wide grain of Z431 was controlled by qGL3, qGW5, etc. By DNA sequencing and qRT-PCR analysis, two best candidate genes for qGL3 and qGW5 were identified, respectively. In addition, pyramid of different QTLs in D1-D3 and T1-T2 showed independent inheritance or various epistatic effects. So, it is necessary to understand all genetic effects of target QTLs for designing breeding. Furthermore, these secondary substitution lines improved the deficiencies of Xihui18 to some extent, especially increasing yield per plant in S1, S3, S5, D1-D3, T1, and T2. [ABSTRACT FROM AUTHOR]

Chalkiness is one of the key determinants of rice quality and is a highly undesirable trait for breeding and marketing. In this study, qWCR7, a major quantitative trait locus (QTL) of white-core rate (WCR), was genetically validated using a BC3F2 segregation population and further fine mapped using a near isogenic line (NIL) population, of which both were derived from a cross between the donor parent DL208 and the recurrent parent ZS97. qWCR7 was finally narrowed to a genomic interval of ~ 68 kb, containing seven annotated genes. Among those, two genes displayed markedly different expression levels in endosperm of NILs. Transcriptome analysis showed that the synthesis and accumulation of metabolites played a key role in chalkiness formation. The contents of storage components and expression levels of related genes were detected, suggesting that starch and storage protein were closely related to white-core trait. Our findings have laid the foundation of map-based cloning of qWCR7, which may have potential value in quality improvement during rice breeding. [ABSTRACT FROM AUTHOR]

Black rice is a rare type of rice germplasm with various health benefits that are largely attributed to anthocyanin pigment accumulation in the pericarps. The anthocyanin biosynthesis in plant tissues is activated mainly by the MBW complexes, consisting of three types of transcription factors R2R3-MYB, bHLH, and WDR. In black rice, the bHLH and WDR components regulating anthocyanin biosynthesis in pericarps have been characterized, while the R2R3-MYB factor remains unknown. By examining the expression correlation between all putative rice MYB genes and anthocyanin biosynthesis–related genes based on transcriptome data of pericarps in combination with further molecular and genetic analysis, we proved that OsMYB3 (LOC_Os03g29614) was the determinant R2R3-MYB gene for anthocyanin biosynthesis in rice pericarps. The expression level of OsMYB3 in pericarps of black rice was significantly higher than that of white rice. The knockout of OsMYB3 in a black rice variety caused significant downregulation of 19 anthocyanin metabolites and many other flavonoids in grains. Our research deepens the understanding of regulatory system for anthocyanin biosynthesis in rice pericarps and provides implications for breeding black rice varieties with high anthocyanin level. [ABSTRACT FROM AUTHOR]

Good eating quality is a highly desirable trait of rice which determines its commercial value and market share. However, the molecular basis of this trait remains largely unknown. Here, three high-quality conventional rice cultivars, including two superior eating quality cultivars Meixiangzhan-2 (MXZ) and Xiangyaxiangzhan (XYXZ), and one ordinary eating quality cultivar Huanghuazhan (HHZ), were analyzed by comparative metabolomics to identify the inherent mechanism for the formation of superior eating quality. The results showed 58.8% of common differential substances between MXZ vs HHZ and XYXZ vs HHZ were enriched in MXZ and XYXZ, whereas 39.2% of them were prominently decreased compared with HHZ, mainly including amino acids, carbohydrates, lipids, phenolamides, and flavonoids, which may be the primary factors leading to the differences of taste and flavor among these three cultivars. We also found that lysine derivatives and fatty acids may have a close relationship with taste. These results above provide important insights into the taste-forming mechanism of rice and will be beneficial for superior eating quality rice breeding. [ABSTRACT FROM AUTHOR]

Rice false smut (RFS), caused by Ustilaginoidea virens, is one of the most destructive grain diseases in rice production worldwide. Hence, to increase the ability of rice resistance to U. virens is a major breeding goal of rice breeders. However, it is difficult to evaluate rice resistance to U. virens. Hence, to clarify the RFS-resistance genetic mechanism is of great significance. In this study, a diversity panel landrace comprising of 315 accessions was identified for resistance against U. virens at reproductive stage in 2017 and 2018. Totally, 58 significant SNPs were distributed on the rice whole genome except chromosome 7, and 3 SNPs associated with three RFS-related traits were identified in 2 years. Haplotype block structure analysis predicted that a total of 15 candidate genes for U. virens resistance were screened based on significant SNPs with minimum P value (− log10P = 13.86). Of which, LOC_Os01g15580, a plant NBS-LRR protein coding gene near the significant SNP chr01_8738751 (12.3 kb), was considered a candidate for key resistance factor in the disease. These findings might provide a new insight into the genetic basis of resistance to rice false smut. [ABSTRACT FROM AUTHOR]

Soil salinity is widespread in rice-producing areas globally, restricting both vegetative growth and grain yield. Improving salt tolerance of rice is a promising approach to meet the increasing food demand. An extensive literature survey indicates that maintaining proper Na+/K+ ratio and reactive oxygen species (ROS) content is the key issues for rice adaption to salt stress. In this review, distinctive from the existing reviews, we mainly discuss recent progresses in identifying the components and pathways involved in the rice response to salt stress and the approaches that can be used for breeding and cultivating salt-tolerant rice, pointing out the potential phytohormonal regulation of the components and the homeostasis of Na+/K+ and ROS. Thus, this review attempts to provide a comprehensive overview of the recent research on rice adaption to salt stress, which may provide guidance for rice breeding to engineer better salt-tolerant rice varieties. [ABSTRACT FROM AUTHOR]

Hybrid rice breeding offers an important strategy to improve rice production, and therefore is crucial for ensuring worldwide food security. Purity of hybrids is a key factor in keeping the high production of hybrid rice. While another important thing is mechanical weeding of hybrid rice, which could greatly release labor from laborious work and cut the production cost. Both of these two problems could be partly resolved by developing glyphosate-tolerant restorer lines. In this study, a novel glyphosate-tolerant gene I.variabilis-EPSPS* was transferred into elite indica restorer line Minghui 86 (MH86) by Agrobacterium-mediated transformation. By Southern blot and inverse PCR analysis, 3 transgenic restorer lines (MY28, MY50, and MY51) with a single copy of I.variabilis-EPSPS* integrated into the intergenic regions were selected from 72 regenerated transgenic plants. The inheritance of I.variabilis-EPSPS* in the 3 transgenic restorer lines was proved to follow Mendelian inheritance by germinating test. In the following generations, according to Southern blot, Northern blot, 3'RACE, and Western blot, I.variabilis-EPSPS* were proved to stably inherit and express in the candidate transgenic restorer lines. At the same time, glyphosate tolerance assay was performed in the field, in which the candidate transgenic restorer lines kept normal agronomic traits under glyphosate treatments with a dosage as high as 8400 g/ha. Therefore, the candidate transgenic restorer lines were highly tolerant to glyphosate. The 3 candidate transgenic restorer lines were respectively hybridized with the male sterile line II-32A, and their hybrids were respectively named as MY28H, MY50H, and MY51H. According to Southern blot and Western blot analysis, I.variabilis-EPSPS* could stably inherit to F1 hybrids and express in these hybrids, which indicated that the true hybrids could be distinguished by I.variabilis-EPSPS*. In the field test, the transgenic hybrids with I.variabilis-EPSPS* could suffer 3360 g/ha glyphosate without the damage of agronomic traits, which indicated the application potential of these hybrids in direct seeding. Collectively, the transgenic glyphosate-tolerant restore lines developed in this study were highly tolerant to glyphosate, and they had potential to be used in commercial production of hybrid rice. [ABSTRACT FROM AUTHOR]

Molecular markers are efficient and essential genotyping tools for molecular breeding and genetic analysis of rice. We developed two 96-plex indica–japonica single nucleotide polymorphism (SNP) genotyping sets for genetic analysis and molecular breeding in rice using the Fluidigm platform. Informative SNPs between indica and japonica were selected from SNP data of the Rice Diversity database, HapRice world SNP data of the Q-TARO database, and our 40 rice cultivar resequencing dataset. SNPs in set 1 were evenly distributed across all 12 rice chromosomes at a spacing of 4–5 Mb between adjacent SNPs. SNPs in set 2 mapped to the long genetic intervals in set 1 and included 14 functional or linked SNPs in genes previously cloned and associated with agronomic traits. Additionally, we used the SNP sets developed in this study to perform genetic diversity analysis of various cultivated and wild rice accessions, construction and validation of a subspecies diagnostic subset, linkage map construction and quantitative trait locus (QTL) analysis of a japonica × indica F2 population, and background profiling during marker-assisted backcrossing. Furthermore, we identified subspecies-specific SNPs and discuss their distribution and association with agronomic traits and subspecies differentiation. Our results indicate that these subspecies-specific SNPs were present in wild rice prior to domestication. This genotyping system will serve as an efficient and quick tool for genetic analysis and molecular breeding in rice. [ABSTRACT FROM AUTHOR]

Heading date, a complex quantitative trait, determines regional adaptability and is associated with grain yield and quality in rice. In this study, we characterized qHd2-1, a minor-effect quantitative locus (QTL) for promoting heading date (by 3–4 days) under long-day (LD) conditions, but not short-day (SD) conditions. The qHd2-1 locus was detected in single segment substitution line (SSSL) N22-1, which was developed using indica 9311 as the donor and japonica Nipponbare (NP) as the recipient. A set of substitution lines were developed from a segregating population derived from a cross between N22-1 and NP. Based on the genotypic identification and phenotypic evaluation of the target substitution lines, qHd2-1 was narrowed down to a 105-kb region between STS2-20 and STS2-22 on the short arm of chromosome 2. Furthermore, qHd2-1 was found to function by upregulating the florigen genes Hd3a and RFT1 during floral induction under LD conditions. Field tests showed that qHd2-1 promotion of heading date affects grain yield‑related agronomic traits, such as plant height, panicle number per plant, and flag leaf size, as well as thousand-grain weight and grain width. Taken together, these findings establish a foundation for cloning this minor-effect QTL involved in heading date, and qHd2-1 could be of great significance in rice breeding to allow the fine-tuning of heading date in rice cultivars. [ABSTRACT FROM AUTHOR]

As a food consumed by more than half of the world's population, rice (Oryza sativa) has always been a hot spot in plant science research. The three most important agronomic traits of rice, the yield, plant height, and flowering time, are controlled by many quantitative trait locus (QTLs). In this study, a newly identified QTL, qHD19, was found to be controlled by a single recessive gene. Using two populations with chromosome segment substitutions, qHD19 was narrowed to a 22.5-kb region containing three putative genes, one of which encoded a ZOS5-02-C2H2 zinc finger protein. This gene was regarded as the qHD19 candidate. Further analysis showed that the amino acid sequence encoded by the qHD19 gene included two amino acid mutations, (84): lysine (L) replaced by phenylalanine (F), and (169): alanine (A) replaced valine (V), and these mutations are expected to significantly alter the functions of the protein. Additionally, the CSSL87 and CSSL88 lines containing the qHD19 gene not only exhibited a shorter plant height but also exhibited a higher yield, which showed that the qHD19 gene presents good application prospects in rice breeding. Taken together, these data indicate that qHD19 probably plays an important role in the signaling network of photoperiodic flowering as well as the regulation of plant height and yield potential. [ABSTRACT FROM AUTHOR]

Two-line hybrid rice breeding, which plays an important role in ensuring food security in China, is one of important approaches to utilize the heterosis in rice. Breeding of photo-thermo-sensitive genic male sterile (PTGMS) lines of two-line hybrid rice with high resistance to diseases and pests is vital for enhancing rice yield stability, reducing environmental pollution, and increasing rice production efficiency. To breed PTGMS rice with resistance to both rice blast and brown planthopper (BPH), four broad-spectrum blast resistance genes Pi9, Pi47, Pi48, and Pi49 and two BPH resistance genes Bph14 and Bph15 were introgressed into a PTGMS line C815S through backcrossing and gene pyramiding coupled with molecular marker-assisted selection (MAS) in this study. Finally, several improved PTGMS lines of C815S which pyramided 1–3 homozygous rice blast resistance genes and two BPH resistance genes were developed. Evaluation of rice blast resistance showed that the improved PTGMS lines were resistant, while C815S was susceptible or only moderately resistant. Assessment of the BPH resistance showed that C815S was highly susceptible, while the improved lines were resistant. The improved lines had similar major agronomic traits and temperature of fertility transition to C815S, and several traits were even better. The newly developed PTGMS lines can be used for breeding of superior two-line hybrid rice or advanced PTGMS lines. [ABSTRACT FROM AUTHOR]

Over the past 20 years, researchers have developed increasingly sophisticated genome information and analytical platforms for rice (Oryza sativa) genetic research. The genetic controls of source capacity include photosynthesis capacity, leaf senescence, canopy architecture, and translocation. Details of these controls have been gradually elucidated using biotechnological approaches and studies of natural genetic resources. These advances have been accompanied by the development of phenotyping methodologies for use under both field and controlled conditions. However, a more comprehensive understanding of the genetic factors that regulate source capacity and their effects on rice yield is required to increase the efficiency of breeding to improve yield. In this review, we summarize the current understanding of the physiological and genetic factors that regulate source capacity gained through biotechnology approaches. We also describe the development of phenotyping methods and recent improvements of our understanding of natural variant genes that regulate source capacity. We conclude that the next challenge to be addressed is closing the gap between understandings of genetic control of source capacity and rice productivity in the field. [ABSTRACT FROM AUTHOR]

An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I)1, qLTGS(I)1–2, qLTG(I)5, qLTGS(I)5, and qLTG(I)7) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), as qLTT1, qLTT2, qLTT3, qLTT5, qLTT6, qLTT8, qLTT9, and qLTT11. A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance. [ABSTRACT FROM AUTHOR]

As more and more re-sequencing genome data in crops were released, SNPs (single nucleotide polymorphisms) are easily achieved for genotyping and show the highest abundance among all kinds of molecular markers. However, high-throughput SNP genotyping methods, such as KASP (Kompetitive Allele Specific PCR), TaqMan, or ARMS (amplification refractory mutation system), are always labor on DNA extraction and depending on expensive equipment. Therefore, most breeders are undergoing the bottleneck of lacking an easy, cost-saving, and stable genotyping system. Here, we report a direct PCR–based medium-throughput SNP marker–assisted selection (D-MAS) system suits available major crops including rice, wheat, maize, and rapeseed. The D-MAS system, which reduces the time of manual operation and result analysis dramatically, contains (1) seedling breeding in greenhouse; (2) high-throughput DNA extraction by alkaline lysis; and (3) gel-free SNP marker detection with 384-well by PARMS (penta-primer amplification refractory mutation) or KASP genotyping system. The stability of alkaline lysis DNA was validated by flexible dilution fold and long storing time under low temperatures. The alkaline lysis DNA from four F2 populations of rice, wheat, maize, and rapeseed showed equal efficiency in SNP calling relative to the ones from cetyl trimethylammonium bromide (CTAB) method. With the alkaline lysis DNA, PAMRS showed denser genotype cluster than KASP. Furthermore, the D-MAS system was adaptive with rice old leaves. The throughput and efficiency of the D-MAS system were validated in the hybrid rice seed purity test with a Xian-Geng-specific SNP marker which is also recommended to select ipa1-2d gene in the rice molecular breeding. In conclusion, we proposed a direct PCR–based SNP calling pipeline, which could be a simple, cheap, and robust standard operation procedure (SOP) of molecular breeding for different crops and get extensive use in most laboratory. [ABSTRACT FROM AUTHOR]

Plant architecture, which consists mainly of plant height, tillering, and panicle morphology, contributes greatly to grain yield in rice. Exploring the molecular mechanisms of rice plant architecture will provide theoretical guidance and valuable gene resources for breeding elite rice varieties with ideal plant architecture. In this review, we emphasize recent progress in elucidating the mechanisms that control rice plant architecture, focusing on tiller number, tiller angle, and panicle branching. Environmental factors influence the plasticity of rice plant architecture, and thus we also discuss the roles of environmental factors in regulating rice plant architecture. [ABSTRACT FROM AUTHOR]

Grain shape is a key factor that influences both grain yield and quality of rice (Oryza sativa L.). In order to elucidate the genetic basis of grain shape, an F2 and derived F2:3 populations were developed from a cross between Guangzhan63-4S (GZ63-4S) and TGMS29, and used in a quantitative trait locus (QTL) analysis. A total of thirty-six QTLs were identified for grain shape and weight, and the phenotypic variance explained by each QTL ranged from 0.88 to 35.70%. Given that most of the QTLs were detected in only one population, a BC1F2 and derived BC1F2:3 populations were constructed with GZ63-4S as the recurrent parent to further verify the QTLs. Seventeen QTLs were validated in at least one population. qGL1.3, the major QTL for grain length in both the F2 and F2:3 populations, contributed 41.16% of the variation in grain length and 35.96% of the variation in 1000-grain weight in a random BC1F3 population, and thus was selected for further fine mapping. Based on progeny tests of 31 recombinants, qGL1.3 was delimited to a region of about 350 kb on chromosome 1. These results could lay the foundation for map-based cloning of qGL1.3 and provide genes or QTLs for breeding rice lines with high grain yield and quality. [ABSTRACT FROM AUTHOR]

Roots are the only organ system to uptake water and nutrients from the soil. The root system is crucial for plants to survive and adapt to environmental stresses. Therefore, the root system architecture (RSA) is an important breeding target for developing climate-resilient rice. Since the rice genome has been completely sequenced, many genes for root development have been cloned and characterized. In addition, with the advances in technologies related to omics analysis, such as high-throughput sequencing, transcriptome analysis of roots has also progressed. In contrast, high-throughput root phenotyping has not been established not only in rice but also in whole plants because roots are hidden underground. This deficiency represents a bottleneck for utilizing an integrated multi-omics approach for molecular breeding of RSA. We first summarized previous transcriptome analyses for root development under various abiotic stresses such as drought, salinity, and heat, and assessed the current status of root phenotyping technology and modeling in rice. This knowledge allowed us to contemplate the possibility of applying an integrated multi-omics dataset from RSA to molecular breeding of climate-resilient rice. [ABSTRACT FROM AUTHOR]

TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY , qDTY , and qDTY , that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2-3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY and qDTY , respectively. QTL class analysis also showed that lines with a combination of qDTY and qDTY consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs. [ABSTRACT FROM AUTHOR]

Glutelin is the most significant seed storage protein and is regarded as an important nutrient quality trait in rice. Research on the genetic basis of the glutelin content distinction in rice will provide more choices for the diets of people with kidney disease and diabetes. The GluA and GluB1 genes play important roles in the process of glutelin synthesis. In this study, 128 Japonica rice accessions with wide geographic distributions were collected to construct the association panel. Among all the 128 accessions, both sequences of the GluA and GluB1 genes were obtained, and nucleotide polymorphisms were detected. A total of 46 SNPs and eight InDels, six SNPs and four InDels were found in the GluA and GluB1 gene sequences, respectively. Eight haplotypes and two haplotypes were classified based on the SNPs in the coding region of the GluA and GluB1 genes, respectively. Moreover, the association of the polymorphic sites in the two genes with glutelin content in the tested population was estimated. The results revealed that five SNPs in the GluA gene, one SNP and one InDel in the GluB1 gene were associated with glutelin content at a significant level ( P < 0.01). Corresponding markers were also designed to check the alleles of GluA and GluB1 genes. These results suggested that polymorphisms in the GluA and GluB1 genes in rice could be utilized in molecular marker-assisted selection to improve the nutrient quality of rice breeding programmes. [ABSTRACT FROM AUTHOR]

WA-CMS system based rice hybrids are widely adopted in many rice growing countries, including India. Even though it is well known that the trait is controlled by mitochondria, the genes underpinning the trait remain enigmatic. In the present study, a complete genome-wide comparative sequence analysis was performed using draft mitochondrial genomes of WA-CMS and male fertile lines in a step-wise manner, progressively covering 5-10 kb every time through BLASTN tool. The sequence polymorphisms identified in different mitochondrial regions were targeted to develop two different sets of dominant PCR-based markers, one consisting of six markers targeting WA-CMS mitochondria, the other set consisting of five markers targeting male fertile mitochondria in addition to development of a set of eight co-dominant PCR-based markers targeting both the genomes. When a set of candidate genes/ORFs reported earlier to be associated with WA-CMS trait in rice were analyzed through RT-PCR of RNA isolated from immature rice florets, it was observed that the chimeric ORF, WA352 is expressed only in WA-CMS line and hybrid (i.e. genotypes containing sterile mitochondria), indicating it's candidacy for the WA-CMS trait. Targeting the functional nucleotide polymorphism between WA-CMS and maintainer mitochondria with respect to WA352, two dominant markers, one targeting sterile and another targeting fertile mitochondria were developed. In addition, a robust, co-dominant functional marker targeting the candidate gene was also developed and validated for its utility in identification of genetic impurities in seed lots of WA-CMS lines. [ABSTRACT FROM AUTHOR]

Starch physicochemical properties strongly influence eating and cooking quality of rice. The cleaved amplified polymorphic sequences, derived CAPS, and InDel markers for 13 starch synthesis-related genes (SSRGs) were developed, and together with markers developed before, there are 35 markers tagged for 23 SSRGs, with each gene tagged with at least one marker. These and 108 other markers were used for association mapping for 20 starch physicochemical property parameters. A total of 64 main-effect loci or quantitative trait locus (QTLs) was detected. In addition, 56 and 62 loci were identified under the Wx and SSIIa background, respectively. Wx was a major main-effect QTL for apparent amylose content (AAC), pasting viscosity, gel texture, and retrogradation property ( P < 0.0001). SSIIa was a major main-effect QTL for pasting temperature, thermal, and retrogradation properties ( P < 0.0001), but it was a minor main-effect QTL for some pasting viscosity parameters, such as BD, CS, Stab, and SBratio. Four other SSRGs, SSIIa, BE1, SSIIc, and GBSSII were detected for AAC under Wx background. Wx was detected for Tc and ΔHg under the SSIIa background. PUL was detected for HD as main-effect QTL and under SSIIa background. AGPL2 and ISA1 were detected, respectively, for ΔHg and retrogradation as main-effect QTL, as well as under both Wx and SSIIa backgrounds. This study suggested that retrogradation properties were mainly controlled by Wx, SSIIa, and ISA1 with the relative effects in the order of SSIIa > Wx > ISA1. These results have direct applications to quality breeding programs. [ABSTRACT FROM AUTHOR]

Rice ( Oryza sativa L.) is a major food component of over half of the world's population, and increased grain yield is a major goal of rice production. Two important yield-related genes are DEP1, regulating inflorescence internode length, and IPA1, involved in plant architecture. The dep1 allele gives rise to a dense, erect panicle shape, while the ipa1 allele leads to a reduced number of tillers and an increased number of grains per panicle. In this study, we focused on the breeding effects of dep1 and ipa1 using two F2 populations derived from cultivars carrying these alleles. Analysis of yield components in the F2 populations revealed that dep1 and ipa1 have contradictory effects, with the exception of number of panicles and spikelet density. The two dep1 and ipa1 alleles can offset each other's negative advantage for some traits. The performance of yield components is consistent with the requirements of ideal plant type in northeast China once the individuals are heterozygous at two loci. By considering genetic analysis data and previous studies, we speculate that DEP1 and IPA1 loci make genetic contributions of additive, dominance and epistasis effects to yield components. Our results should provide a valuable reference for developing hybrid japonica rice by direct application of F1 plants heterozygous at the two loci and for shortening the breeding period for conventional japonica rice by rapidly fixing superior genotype combinations in early hybrid generations. [ABSTRACT FROM AUTHOR]

Stigma exsertion rate is a key factor which influences the efficiency of hybrid seed production in rice. To clarify the genetic basis of stigma exsertion rate, a recombinant inbred line population was developed from two superior rice cultivars, Zhongguo Xiangdao (ZX) and Chuanxiang 29B (CX29B), and a total of 11 quantitative trait loci (QTLs) for stigma exsertion rate were detected over 2 years. Two QTLs on chromosome 1 and four QTLs on chromosome 6 formed two QTL cluster regions, qSe1 and qSe6, respectively. To further validate the effect of qSe1 and qSe6, the near-isogenic lines (NILs) of the two QTL cluster regions were constructed with the genetic background of CX29B. Compared to CX29B, CX29B ( qSe1), the NIL carrying homozygous qSe1 regions from ZX, showed a dual stigma exsertion rate increased by 18.35 % and a single stigma exsertion rate increased by 16.24 %; in contrast, CX29B ( qSe6), the NIL carrying homozygous qSe6 regions from ZX, showed a dual stigma exsertion rate decreased by 16.87 % and a single stigma exsertion rate decreased by 20.47 %. Therefore, the qSe1 region from ZX and the qSe6 region from CX29B have positive effects on improvement of stigma exsertion rate and would be very useful in rice breeding. [ABSTRACT FROM AUTHOR]

Improvement of eating and cooking quality (ECQ) traits is a major breeding target in indica rice due to market demand. In this study, amylose content, gel consistency, gelatinization temperature and 15 parameters from the viscosity profile were analyzed for quantitative trait loci (QTLs) with main effect, epistatic effects and their environmental interactions with ECQ, using 237 recombinant inbred lines (RILs) derived from a cross between indica cultivars Huahui 3 and Zhongguoxiangdao. Sixty-six QTLs were found across 2 years, of which 17 loci were detected in both years. No QTL was detected at the Wx locus, possibly because of allelism between the parents. A QTL cluster in the interval ALK6-RM549 on chromosome 6 had the largest effect on alkali spreading value, pasting time, time needed from initial viscosity increase to peak viscosity, pasting temperature, temperature needed from initial viscosity increase to peak viscosity, and pasting viscosity, and a minor effect on six traits (parameters): gel consistency, amylose content, peak viscosity, cool paste viscosity, breakdown viscosity and setback viscosity. Moreover, the Alk gene was responsible for two traits studied for the first time, namely peak temperature and pasting viscosity, controlled by QTLs qBAtime6 and qVA6, respectively. QTL clusters on other chromosomes showed similar characteristics to the Alk locus, although the variations explained were relatively minor. The OsBEIIb gene locus is linked to the interval RM301-RM424, which defined an important QTL cluster on chromosome 2. Moreover, a study using the same RIL population showed that a QTL for protein content and Rapid Visco Analyzer parameters was tightly linked to the same gene and directly affected ECQ. These findings not only demonstrate the complexity of ECQ, but also have important implications for map-based cloning of the underlying genetic factors and for breeding for rice quality. [ABSTRACT FROM AUTHOR]

Phytic acid ( myo-inositol-1,2,3,4,5,6-hexa kisphosphate or InsP) accounts for 75-85 % of the total phosphorus in seeds. Low phytic acid ( lpa) mutants exhibit decreases in seed InsP with corresponding increases in inorganic P which, unlike phytic acid P, is readily utilized by humans and monogastric animals. Since InsP may also reduce the bioavailability of essential mineral cations, development of lpa seed crops for animal feeds and whole-grain consumers is of significant interest and requires better understanding of the metabolism of InsP and the role it plays in other plant processes. To date, well over 20 lpa mutants have been reported in a number of species, most of which have been identified through forward genetic screens. In this study, we used a publicly available rice Targeting of Induced Local Lesions IN Genomes (TILLING) resource to identify four novel lpa mutations, two in one member of the inositol(1,3,4)P 5/6-kinase (ITPK) gene family (LOC_Os09g34300) and two in a multi-drug resistance-associated protein (MRP) gene (LOC_Os03g04920). The mutations in the ITPK gene resulted in significant reductions in InsP (46 and 68 %), while those found in MRP gene were more modest (20 and 30 %). Evaluation of these lines indicates that one of the ITPK mutants (46 % InsP reduction) and both MRP mutants are similar to wild-type plants in seed weight, germination, and seedling growth. The four mutants identified here represent new resources for the genetic dissection of phytic acid metabolism in rice and the development of germplasm and strategies for breeding lpa rice varieties. [ABSTRACT FROM AUTHOR]

The eating and cooking qualities of rice grains are the major determinants of consumer preference and, consequently, the economic value of a specific rice variety. These two qualities are largely determined by the physicochemical properties of the starch, i.e. the starch composition, of the rice grain. In our study, we determined the genetic factors responsible for the physicochemical properties of starch in recombinant inbred lines (RILs) of japonica cv. Tainung 78 × indica cv. Taichung Sen 17 (TCS 17) cultivated over two crop seasons by examining palatability characteristics and several Rapid Viscosity Analyzer (RVA) parameters. Thirty-four quantitative trait loci (QTLs), each explaining between 1.2 and 78.1 % phenotypic variation, were mapped in clusters on eight chromosomes in 190 RILs genotyped with 139 markers. Ten pairs of QTLs were detected in the two environments, of which seven were in agreement with previous findings, suggesting that these QTLs may express stable experimental populations across various environments. Waxy ( Wx), which controls amylose synthesis, was determined to be a primary gene regulating the physicochemical properties of cooked rice grains, as indicated by the presence of a major QTL cluster on chromosome 6 and by marker regression analysis. Six starch synthesis-related genes (SSRGs) which were located in the QTL intervals significantly differed in terms of gene expression between the two parents during grain-filling and were important genetic factors affecting physicochemical properties. The expression of four genes, PUL, ISA2, GBSSI, and SSII- 3, was significantly upregulated in TCS 17, and this expression was positively correlated with six traits. The effects of the six SSRGs and gene interaction depended on genetic background and environment; grain quality may be fine tuned by selecting for SBE4 for japonica and PUL for indica. We provide valuable information for application in the breeding of new rice varieties as daily staple food and for use in industrial manufacturing by marker-assisted selection. [ABSTRACT FROM AUTHOR]

A recombinant inbred population developed from a cross between high-yielding lowland rice ( Oryza sativa L.) subspecies indica cv. IR64 and upland tropical rice subspecies japonica cv. Cabacu was used to identify quantitative trait loci (QTLs) for grain yield (GY) and component traits under reproductive-stage drought stress. One hundred fifty-four lines were grown in field trials in Indonesia under aerobic conditions by giving surface irrigation to field capacity every 4 days. Water stress was imposed for a period of 15 days during pre-flowering by withholding irrigation at 65 days after seeding. Leaf rolling was scored at the end of the stress period and eight agronomic traits were evaluated after recovery. The population was also evaluated for root pulling force, and a total of 201 single nucleotide polymorphism markers were used to construct the molecular genetic linkage map and QTL mapping. A QTL for GY under drought stress was identified in a region close to the sd1 locus on chromosome 1. QTL meta-analysis across diverse populations showed that this QTL was conserved across genetic backgrounds and co-localized with QTLs for leaf rolling and osmotic adjustment (OA). A QTL for percent seed set and grains per panicle under drought stress was identified on chromosome 8 in the same region as a QTL for OA previously identified in three different populations. [ABSTRACT FROM AUTHOR]

Discovery of new fragrance alleles provides important genetic resources for breeding fragrant rice. In this study, a hybrid complementation test demonstrated the association of a new fragrance allele without mutation in the coding region with flavor formation in a fragrant rice variety Nankai 138. The new allele ( badh2- p- 5′UTR) has a 3-bp deletion in the 5′ untranslated region and an 8-bp insertion in the promoter (−1,314 site upstream from the initiation codon). Surprisingly, we found that there is also an 8-bp insertion in the promoter of the badh2- E7 allele. We developed a new sequence tagged site functional marker to identify the badh2- p- 5′UTR and badh2- E7 alleles according to the 8-bp insertion in their promoters. A cleaved amplified polymorphic sequence ( AluI) functional marker targeting a common base substitution in the intron 2 of three badh2 alleles, viz. badh2- p- 5′UTR, badh2- E7 and badh2- E2, was developed to identify diverse genotypes for fragrance in rice. Based on the results of sequence alignments among the three badh2 alleles, we suggest that the badh2- E7 and badh2- p- 5′UTR alleles may have the same genetic origin. In addition, the genetic distance between the badh2- E7 and badh2- p- 5′UTR alleles may be closer than that between the badh2- E2 and the badh2- p- 5′UTR alleles, or between the badh2- E2 and the badh2- E7 alleles. [ABSTRACT FROM AUTHOR]

Plants adapt to abiotic stress by undergoing diverse biochemical and physiological changes that involve hormone-dependent signaling pathways. The effects of plant hormones can be mimicked by exogenous chemical regulators such as herbicide safeners, which not only enhance stress tolerance but also confer hormetic benefits such as increased vigor and yield. In this study, rice plants growing in normal and saline soils were exposed to abscisic acid (ABA), the safener cyprosulfamide or both compounds together. We found that cyprosulfamide, either alone or in combination with ABA, protected the plants from salinity stress and induced vigorous growth, including the formation of new tillers and early flowering. Proteomic analysis identified several proteins that were induced by stress and/or the chemical treatments, including the late embryogenesis abundant protein OsLEA3, a putative mitochondrial translocase and a putative fumarylacetoacetate hydrolase. The corresponding genes were induced by stress and/or the individual chemical treatments, but expression dropped back when the stress was removed. However, the combination of ABA and cyprosulfamide prolonged the expression of all three genes beyond the stress period, and allowed the plants to maintain their enhanced growth characteristics. These data support a model involving cooperation between the cyprosulfamide and ABA signaling pathways. Accordingly, it was found that cyprosulfamide induces ABA synthesis more robustly than salinity stress, allowing the two regulators to converge on certain downstream target genes. We discuss the impact of our results on current models for the hormonal regulation of stress response pathways in rice and other plants. [ABSTRACT FROM AUTHOR]

The use of broad-spectrum R genes is an effective way to achieve durable resistance against rice blast ( Magnaporthe oryzae Couch, anamorph: Pyricularia oryzae Cavara) in rice ( Oryza sativa L.). We previously surveyed the diversity of blast resistance in 948 rice varieties and found a Myanmar rice landrace, Haoru (International Rice Research Institute genebank acc. no. IRGC33090), with broad-spectrum resistance against the standard differential blast isolates. Here, we examined the genetic basis of Haoru's broad-spectrum resistance by using the standard blast differential system consisting of the standard isolates and differential varieties. For genetic analysis, we used a BC1F1 population and BC1F2 lines derived from crosses of Haoru with a susceptible variety, US-2. Co-segregation analysis of the reaction pattern in the BC1F1 population against the 20 standard isolates suggested that Haoru harbors three R genes. By using bulk-segregant and linkage analysis, we mapped two of the three R genes on chromosomes 12 and 6, and designated them as Pi58(t) and Pi59(t), respectively. Pi58(t) and Pi59(t) were differentiated from other reported R genes using the standard differential system. The estimated resistance spectrum of Pi58(t) corresponded with that of Haoru, suggesting that Pi58(t) is primarily responsible for Haoru's broad-spectrum resistance. In addition, Pi59(t) and the third gene were also proven to be new and useful genetic resources for studying and improving blast resistance in rice. [ABSTRACT FROM AUTHOR]

Rice black streaked-dwarf virus (RBSDV) disease is recently expanding in southern China and poses a serious threat to rice crops. Few studies related to the genetics and breeding of RBSDV resistance have been reported. We have previously mapped a number of quantitative trait loci (QTLs) for RBSDV resistance by using a recombinant inbred line population of 'Zhenshan 97' (ZS97, susceptible)/'Minghui 63' (MH63, resistant) with natural infection data in two locations. In the present study, we confirmed the presence of a number of resistant QTLs on chromosomes 6, 7, and 9 from MH63 by using the same population in four different locations. We then focused on a major QTL, qRBSDV- 6, on chromosome 6 and introduced it into a highly susceptible japonica rice variety, 'Huaidao 5', using MH63 as the donor via marker-assisted selection, to generate seven backcross inbred lines (BILs). Natural infection and artificial inoculation-based tests revealed that all of the BILs had a significantly higher resistance to RBSDV than the recurrent parent. These results demonstrate that qRBSDV- 6 is a stable major resistance QTL of high breeding value. We also constructed a set of chromosome segment substitution lines (CSSLs) specific to the qRBSDV- 6 region and these used as fine mapping population. Combining the genotypes of CSSLs with the phenotypes from natural infection data in a highly RBSDV epidemic area during two different sowing seasons, we were able to precisely map qRBSDV- 6 to the markers S18 and S23 at a physical distance of 627.6 kb on the Nipponbare reference genome. [ABSTRACT FROM AUTHOR]

Hybrid rice based on heterosis can significantly increase rice yield compared to inbred rice. Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv . oryzae ( Xoo) is one of the most destructive bacterial diseases that affect hybrid rice production. To breed a broad-spectrum and high disease resistance to BB in hybrid rice, we introduced the Xa4, Xa21 and Xa27 genes into the restorer lines of Mianhui 725 or 9311 genetic backgrounds and pyramided the three R genes in the progeny derived from the cross between the two lines. A near-isogenic line of the Xa27 gene in the genetic background of 9311 [9311( Xa27)] and another line with the Xa4 and Xa21 genes in the genetic background of Mianhui 725 (WH421) were firstly developed through marker-assisted selection. A new restorer line carrying Xa4, Xa21 and Xa27, designated as XH2431, was selected from the F8 progeny of the cross between 9311( Xa27) and WH421 through marker-assisted breeding and pedigree selection. XH2431 and II You 2431, the hybrids derived from cytoplasmic male-sterile line II-32A and restorer line XH2431, conferred high resistance to all 23 Xoo strains collected from 10 countries. XH2431 restored the fertility of II-32A to the normal level in the F1 generation. In addition, II You 2431 showed good agronomic traits under greenhouse conditions. The development of XH2431, 9311( Xa27) and WH421 provides a set of restorer lines with broad-spectrum and enhanced resistance to BB for hybrid rice. [ABSTRACT FROM AUTHOR]